Maintenance of thymus homeostasis is a delicate interplay involving hormones, neurotransmitters and local microenvironmental proteins, as well as saccharides, acting on both thymocytes and stromal cells. Disturbances in these interactions may lead to alterations on thymocyte development. We previously showed that galectin-3, a β-galactoside-binding protein, is constitutively expressed in the thymus, interacting with extracellular matrix glycoproteins and acting as a de-adhesion molecule, thus modulating thymocyte-stromal cell interactions. In this work, we aimed to investigate the participation of galectin-3 in the maintenance of thymus homeostasis, including hormonal-mediated circuits. For that, we used genetically engineered galectin-3-deficient mice. We observed that the thymus of galectin-3-deficient mice was reduced in mass and cellularity compared to wild-type controls; however, the proportions of different thymocyte subpopulations defined by CD4/CD8 expression were not changed. Considering the CD4−CD8− double-negative (DN) subpopulation, an accumulation of the most immature (DN1) stage was observed. Additionally, the proliferative capacity of thymocytes was decreased in all thymocyte subsets, whereas the percentage of apoptosis was increased, especially in the CD4+CD8+ double-positive thymocytes. As glucocorticoid hormones are known to be involved in thymus homeostasis, we evaluated serum and intrathymic corticosterone levels by radioimmunoassay, and the expression of steroidogenic machinery using real-time PCR. We detected a significant increase in corticosterone levels in both serum and thymus samples of galectin-3-deficient mice, as compared to age-matched controls. This was paralleled by an increase of gene transcription of the steroidogenic enzymes, steroidogenic acute regulatory protein (Star) and Cyp11b1 in thymus, 11β-Hydroxysteroid Dehydrogenase (Hsd11b1) in the adrenal, and Cyp11a1 in both glands. In conclusion, our findings show that the absence of galectin-3 subverts mouse thymus homeostasis by a mechanism likely associated to intrathymic and systemic stress-related endocrine circuitries, affecting thymocyte number, proliferation and apoptosis.